Time for another Q&A post (yes, I'm finally doing an effort in replying your long overdue questions!).
Here's a question I received a few months ago:
While reading any phd file you usually highlight the important points from that file. How do you manage this thing as there are number of different papers which you have read and later if you need any particular piece of information then how do you search for that one? Maybe you highlighted that part but you have forgotten in which paper you read that particular info
Any idea regarding this?
At that time, I replied very short:
You can for example add notes and keywords in Endnote
So, let me expand on this question, and break this question down into some parts.
First of all, "you usually highlight the important points".
Well, highlighting in a PDF on your computer is not necessarily the most efficient way of absorbing the material. One of my favorite academic bloggers, Dr. Raul Pacheco-Vega, has written a number of excellent posts on taking notes while reading. I recommend you read this post about writing memorandums (which also answers your question in terms of filing your notes!), this post with links to previous posts about the literature review (assuming that you are currently working on your literature review), this post about using colors for highlighting , this post about highlighting and note-taking, and finally this post about taking notes by hand.
Dr Pacheco-Vega's method is brilliantly organized. Mine is certainly more haphazard. Sometimes I will print an article, and my notes will be limited to doodling in the margin (I mostly draw load paths when I try to understand how a structure works). I don't write memorandums nor summaries - but I must say that my memory works like a sponge: I read a paper and I will remember the most important parts of it.
Next topic "there are a number of different papers which you have read"
Don't wait until you've read all the papers on your desk to start writing the document in which you want to process this information. Start from the beginning. Focus on contradictions and links between the papers. I've written previously on how to deal with a large amount of literature.
Final topic "you have forgotten in which paper you read that particular info"
Here's where a good paper management system comes into place. You can use software like Endnote, Zotero, Mendeley, ... to do the job for you. If you do so, I suggest you make sure you have your database as complete as possible: add research notes and keywords if you want to be able to find the paper back, and make sure you add the abstract. I suggest you order the physical copies by alphabet of first author, so you can find your physical copy with your scribbled notes back whenever you need it.
For more tips for your literature review, go here and here.